This is a cool idea - in fact a friend of mine suggested I should make something similar the other day, so I'll have to send him a link to yours. Most of the puzzles stumped me, sadly. I tried turning the reactor all off and all on and neither seemed to work. Maybe I was just supposed to leave it on without pressing "execute".
I LOVED the witty lines. Very funny writing. "Don't worry, that's execute as in 'run'". Fabulous.